ABC-transporters prevent the access of antiepileptic drugs into brain parenchyma, which partly explains why seizures are frequently refractory to AEDs treatment. Overexpression of ABC-transporters and stem-cell markers including CD34, have been detected in malformations of cortical development (MCD) and brain tumors. ABC-transporters are constitutively expressed during maturation of normal progenitor stem-cells and cancer stem-cells. These abnormal/immature cells of MCD or brain tumors play an active role in the epileptogenesis but the precise nature of this phenomenon is unclear. Irrespective of their property in the pharmacoresistance, ABCB1-transporter P-glycoprotein also plays a role in the membrane depolarization, suggesting that constitutive P-glycprotein overexpression in MCD and brain tumors could explain their epileptogeneic properties. MCD as wells as brain tumors arise from abnormal progenitor cells, where ABC-t together with others stem cell markers, could help to better identification of these abnormal progenitor cells and serve as biomarker of risk for seizure relapse after epilepsy surgery.